American spies have detected “a real decrease in quality” of communications between targets such as Ayman al-Zawahiri, the jihadist network’s leader, US officials complained to The New York Times.

In August, the Obama administration abruptly decided to close US embassies in 19 countries and issue a broad travel warning to Americans after intercepting an al-Qaeda communication.

Zawahiri, the group’s leader since the death of Osama bin Laden, reportedly issued “clear orders” to Nasir al-Wuhaysi, head of its Yemen-based branch, to carry out an attack, according to McClatchy Newspapers.

The detail, said to relate to the most serious al-Qaeda plot since the attacks of September 11, 2001, was sourced to “an official who’d been briefed on the matter in Sanaa, the Yemeni capital”.

It was subsequently reported that the order was intercepted during a conference-call-style group conversation between Zawahiri, Wuhaysi and other al-Qaeda leaders.

Since then, there has been a “sharp drop in the terrorists’ use of a major communications channel,” The New York Times reported.

The sharpest decline in messaging was said to have been among al-Qaeda operatives in Yemen. However one official said “the switches weren’t turned off” completely.

The officials said the leak about the Yemen plot presented a more serious setback to US intelligence than the actions of Edward Snowden, the former National Security Agency contractor who released a cache of secret documents on US intelligence to the media after fleeing his job.

Rather than detecting a decline in communications due to Mr Snowden’s leaks, “analysts have detected terrorists mainly talking about the information that Mr Snowden has disclosed.”

Separately, at least three Yemeni soldiers were killed and six others wounded on Monday when a group of suspected al Qaeda militants disguised as security personnel attacked an army base in the southeastern city of al-Mukalla, a military official said.

The official said soldiers were still trading fire with the militants inside the base.

"Some of the attackers managed to infiltrate into the base," the official said. "They caused confusion because soldiers at the base thought they were being attacked by members of the Central Security apparatus."

Zawahiri issued his first specific guidelines for jihad earlier this month, urging restraint in attacking other Muslim sects and non-Muslims and in starting conflicts in countries where jihadis might find a safe base to promote their ideas.

The document, published by the SITE monitoring service, provides a rare look at al Qaeda's strategy 12 years after the September 11 attacks on the United States and the nature of its global ambitions from North Africa to the Caucasus to Kashmir.

While al-Qaeda's military aim remained to weaken the United States and Israel, Zawahri stressed the importance of "dawa", or missionary work, to spread its ideas.

"As far as targeting the proxies of America is concerned, it differs from place to place. The basic principle is to avoid entering into any conflict with them, except in the countries where confronting them becomes inevitable," he said.

Those comments are particularly relevant for North Africa, where many analysts believe al Qaeda is using the less restrictive environment which followed the 2011 Arab uprisings to seek new followers, often through local alliances, while avoiding drawing attention to itself by eschewing attacks.

"Our struggle is a long one, and jihad is in need of safe bases," Zawahiri said in his "general guidelines for jihad" posted on jihadi forums.

Senior American officials say that Mr. Snowden’s disclosures have had a broader impact on national security in general, including counterterrorism efforts. This includes fears that Russia and China now have more technical details about the N.S.A. surveillance programs. Diplomatic ties have also been damaged, and among the results was the decision by Brazil’s president, Dilma Rousseff, to postpone a state visit to the United States in protest over revelations that the agency spied on her, her top aides and Brazil’s largest company, the oil giant Petrobras.

On September 20, suspected Al-Qaeda fighters killed at least 56 soldiers and police in coordinated dawn attacks in Shabwa province further west.

That was the deadliest day for the Yemeni security forces since the army recaptured a string of southern towns from the jihadists in a major offensive last year.

Washington regards Al-Qaeda in the Arabian Peninsula as the global jihadist network's most dangerous affiliate and has stepped up its drone strikes against the group in recent weeks.